Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A1 F1 I2 R1 884 257.2 12958910 96.9% 12557183 93.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,008,404 +G coding (487/516 nt) b4555 → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,008,4021.G98.6% 241.7 / ‑3.7 70coding (485/516 nt)b4555hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base G (30/39);  total (30/40)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCTGGAAGTGATGGCGGGCGGCGTTTC‑AAAGGCCATGCGCTGGAAG‑GCTGGCG‑‑‑‑A‑‑‑‑ACT‑GG‑CTACAG‑CTGAAGGATTG‑ATTGCGTT‑‑GTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGAAA‑GCTGCATTATG  >  NC_000913/4008346‑4008483
                                                                   |                                                                                        
tCTGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGtt                                                            >  1:1148257/1‑93 (MQ=255)
tCTGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGtt                                                            <  1:5720128/93‑1 (MQ=255)
tCTGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGtt                                                            <  1:2423527/93‑1 (MQ=255)
tCTGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGtt                                                            <  2:3052296/93‑1 (MQ=255)
  tGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGtttg                                                          <  2:4945205/93‑3 (MQ=255)
  tGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGtttg                                                          <  1:5203346/93‑3 (MQ=255)
  tGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGtttg                                                          >  1:5279004/1‑91 (MQ=255)
  tGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGtttg                                                          <  1:6351818/93‑3 (MQ=255)
  tGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGtttg                                                          <  2:2720365/93‑3 (MQ=255)
  tGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGtttg                                                          <  2:2612051/93‑3 (MQ=255)
   ggAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGtttgg                                                         >  2:2368692/1‑90 (MQ=255)
   ggAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGtttgg                                                         <  1:1390840/93‑4 (MQ=255)
    gAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCG‑‑‑‑AAGAGACTGGG‑CTACAGCCTGAAGGATTGTATTGCGtttggg                                                        >  2:3799169/1‑89 (MQ=255)
    gAAGTGATGGCGGGCGGCGTCTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGtttggt                                                        <  2:2138944/93‑5 (MQ=255)
          aTGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACggg                                                  <  2:3643840/93‑1 (MQ=255)
          aTGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACggg                                                  >  1:4895227/1‑93 (MQ=255)
          aTGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACggg                                                  <  1:4539782/93‑1 (MQ=255)
           tGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGa                                                 <  2:2652227/93‑1 (MQ=255)
            ggcgggcgGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGAt                                                <  1:1612030/93‑1 (MQ=255)
            ggcgggcgGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGAt                                                <  2:1677885/93‑1 (MQ=255)
            ggcgcgcgGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACT‑GGCCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGAt                                                <  1:819012/93‑1 (MQ=255)
             gcgggcggCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATg                                               <  2:4096718/93‑1 (MQ=255)
              cgggcggCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGa                                              <  1:3726700/93‑1 (MQ=255)
               gggcggCGTTTCAAAAGGGCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGaa                                             <  2:3318022/93‑1 (MQ=255)
               gggcggCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGaa                                             <  1:3501601/93‑1 (MQ=255)
               gggcggCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGaa                                             >  2:201803/1‑93 (MQ=255)
                ggcggcGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAac                                            <  2:2472633/93‑1 (MQ=255)
                ggcggcGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAac                                            >  2:4169501/1‑93 (MQ=255)
                ggcggcGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAac                                            <  1:4668012/93‑1 (MQ=255)
                ggcggcGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAac                                            >  2:2412012/1‑93 (MQ=255)
                ggcggcGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAac                                            >  2:1145412/1‑93 (MQ=255)
                 gcggcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAacg                                           <  1:3946254/93‑1 (MQ=255)
                 gcggcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAacg                                           <  2:733206/93‑1 (MQ=255)
                  cggcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAacga                                          <  1:3061014/93‑1 (MQ=255)
                  cggcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAacga                                          <  1:5029312/93‑1 (MQ=255)
                  cggcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAacga                                          <  1:3733356/93‑1 (MQ=255)
                   ggcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAacgac                                         >  1:838731/1‑93 (MQ=255)
                   ggcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAacgac                                         <  2:6349720/93‑1 (MQ=255)
                   ggcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAacgac                                         <  1:1387788/93‑1 (MQ=255)
                   ggcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAacgac                                         <  2:6002290/93‑1 (MQ=255)
                   ggcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAacgac                                         <  1:2279083/93‑1 (MQ=255)
                   ggcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAacgac                                         >  2:506903/1‑93 (MQ=255)
                    gcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAacgacg                                        >  1:550341/1‑93 (MQ=255)
                    gcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAacgacg                                        >  1:1938896/1‑93 (MQ=255)
                    gcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAacgacg                                        <  1:1704662/93‑1 (MQ=255)
                     cgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGc                                       <  2:2284238/93‑1 (MQ=255)
                      gTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGcc                                      >  2:1050943/1‑93 (MQ=255)
                      gTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGcc                                      >  2:5795906/1‑93 (MQ=255)
                      gTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGcc                                      >  2:3054417/1‑93 (MQ=255)
                      gTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGcc                                      <  2:3718784/93‑1 (MQ=255)
                          caaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGaaa                                  <  1:2486652/91‑1 (MQ=255)
                           aaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAAt                                 >  2:2970238/2‑93 (MQ=255)
                           aaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAAt                                 >  2:269946/2‑93 (MQ=255)
                            aaaGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATg                                >  2:1611781/1‑93 (MQ=255)
                             aaGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGc                               >  1:1121834/1‑93 (MQ=255)
                             aaGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGc                               >  1:5171996/1‑93 (MQ=255)
                             aaGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGc                               >  1:501772/1‑93 (MQ=255)
                             aaGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGc                               <  2:4329317/93‑1 (MQ=255)
                              aGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCt                              >  1:4406304/1‑93 (MQ=255)
                              aGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCt                              <  2:871705/93‑1 (MQ=255)
                              aGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCt                              >  2:6392472/1‑93 (MQ=255)
                              aGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCt                              >  1:3051662/1‑93 (MQ=255)
                              aGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCt                              >  1:4138537/1‑93 (MQ=255)
                              aGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCt                              >  1:4308666/1‑93 (MQ=255)
                              aGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCt                              >  1:5530256/1‑93 (MQ=255)
                              aGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCt                              >  1:616170/1‑93 (MQ=255)
                              aGGCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCt                              >  2:2466575/1‑93 (MQ=255)
                               ggCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTg                             <  1:3417397/93‑1 (MQ=255)
                               ggCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTg                             >  1:317445/1‑93 (MQ=255)
                               ggCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTg                             <  2:3128863/93‑1 (MQ=255)
                               ggCCATGCGCTGGAAGCGGTGGCGAAGAA‑‑‑‑ACTGGG‑CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTg                             <  2:1872397/93‑1 (MQ=255)
                                                          aa‑‑‑‑aCT‑GGTCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACTGGATGACCGACGTCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATg  <  2:5137555/92‑1 (MQ=255)
                                                                   |                                                                                        
TCTGGAAGTGATGGCGGGCGGCGTTTC‑AAAGGCCATGCGCTGGAAG‑GCTGGCG‑‑‑‑A‑‑‑‑ACT‑GG‑CTACAG‑CTGAAGGATTG‑ATTGCGTT‑‑GTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGAAA‑GCTGCATTATG  >  NC_000913/4008346‑4008483

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A